Season 1-5 of Stargate Atlantis
by Supreme Commander
Summary: this is my version of stargate Atlantis and will epiosdes from the tv show as well as a few other episodes. New Characters along with the old. hope you enjoy. this is also to prepare you for Season 6-10 with Colonel Horton who's actually a Lantian/wraith from the Lantian Royal Family and the Wraith Royal Family.
1. Chapter 1: Rising

Stargate Atlantis

Season I

Chapter One

 **Disclaimer: SGA is not mine, the story I'm writing is following the season but I'm only dong those that I enjoyed. It has some new characters that are mine. I really hope you enjoy the story and please read and review.**

 **Author Note: like I said this follows Seasons 1-5 and want be every episode, new characters are added such as Colonel Horton is the military commander while Major/Lieutenant Colonel John Sheppard will be his second in command. Other new characters will be in later episodes of the seasons along with a few new episodes. Colonel Horton accompanies John's team on many mission being the 5** **th** **man on the team but also goes on his own assignments.**

 **Author Note: Colonel Horton is a Half Lantian/Half Wraith born from two royal families during the first Lantian-Wraith War. More about him will be and later chapters.**

Introduction

Atlantis several million years ago

A small spaceship flies over the top of clouds. As it reaches the edge of the clouds, we see a large star-shaped city on the ground, surrounded by a forcefield. Inside the city, a man and a woman dressed in futuristic-looking clothes stand at a window watching the ship approach, then turn and gaze at each other. The woman is Ayiana Outside the window, the small ship bursts through the forcefield and comes in to land. The man and Ayiana gaze at each other for a moment longer, and then the man turns and walks away. Ayiana watches him go, a look of longing or loss on her face.

After a few moments she turns to look out of the window again. Behind her is the Ancient Control Chair outside, the city begins to rise into the air, leaving behind only the area that Ayiana is standing in. Once clear of the central area, engines kick in and the city shoots up into the sky.

ANTARCTICA, PRESENT DAY.

A small dome and outbuildings where constructed where the ancient platform was found by General Jack O'Neill and his team when he had the ancient knowledge downloaded into his head. Inside the dome an elevator descends down to the level where the Control Chair was found. The elevator arrives and there's a hive of activity in a large area carved out of the rock. Many scientists are working down there. As the doors to the elevator open, a little way away a man is working on an unused attack drone from amongst those which took down Anubis's fleet. Doctor Elizabeth Weir, formerly Head of Stargate Command, comes out of the elevator and a scientist hands a computer pad to her.

"This is Operations. General O'Neill is en route. He is Twenty minutes out," a voice over tannoy. Doctor Weir walks across the room. The man working on the drone is Doctor Peter Grodin, an Englishman, looks up and sees her.

"Doctor Weir, good to see you again," Grodin says to her.

"Peter, it's good to see you too?" She writes something on the computer pad puts it down and walks over to the Control Chair. Doctor Carson Beckett, a Scottish man, is sitting in the Chair with Doctor Rodney McKay standing beside him.

"You see nothing," Carson says to them. He gets out of the chair and starts to walk away.

"Carson. Get back here," McKay calls after him.

"I could sit in that chair all bloody day long and nothing would happen. It's a waste of time. Excuse me, Doctor Weir," he tells them. He walks away.

"He's not even trying," McKay says to Doctor Elizabeth Weir.

"But he's the one who discovered the gene this technology responds to." Weir says to him.

"Yeah, well, he said he wished he never had it."

"We've only found a handful of people who are genetically compatible with the Ancient technology and despite your heroic efforts to interface ours with theirs; we need every one of them to sit in this Chair, including Doctor Beckett. I kind of wishing Colonel Horton was here we no he has the gene, but he's busy on an off world mission helping Teal'c and an SG team deal with some of Anubis supporters."

"When should he return?"

"Sometime later on today or first thing tomorrow morning," she replies. "Why doesn't Carson not want to keep trying to activate this chair?"

"He's afraid of that thing," Rodney says.

"This Chair controls the most powerful weapons known to humankind. I'm afraid of the thing. But every time someone sits in it we learn something new about the Ancients who built this outpost. Doctor Beckett should be proud he's genetically advanced."

"It's not more advanced. It's a random characteristic."

"This really bothers you, this whole gene thing, huh?"

"Oh, clearly I am overcome with envy," McKay says. Doctor Daniel Jackson enters.

"Ah, just the people I need to see," Jackson says. He turns and walks away again. Weir and McKay look at each other. Weir and McKay follow Daniel leads the other two into a lab. "We've gotten closer and closer to finding the location of the Lost City but it turns out we've been looking in the wrong place all along." He walks over to a whiteboard on which are drawn six Stargate coordinates with the numbers 1-6 above them. "Now, we thought we had a Stargate address - six symbols representing coordinates in space that determine the location of the planet the Ancients went to after they left Antarctica. Now, recently we determined a seventh symbol." He picks up a pen and draws the symbol representing Earth on the board to the right of the other symbols.

"The point of origin, Earth," Weir says.

"That's not it," he says.

"Then your address must be incorrect," Rodney says.

"Not incorrect… incomplete," Jackson says. He draws another symbol in between the sixth symbol and the Earth symbol.

"What are you saying, Doctor Jackson?" Weir asked. Daniel numbers the newest symbol 7 and the Earth symbol 8.

"It's an eight symbol address. What we're looking for may be further away than we ever imagined, but it's not out of reach."

"Atlantis!" Rodney says.

"Atlantis. I think we can go there," Jackson says.

A helicopter flies over the snow of Antarctica. Major John Sheppard is flying it, taking General Jack O'Neill to the outpost. General O'Neill and Major Sheppard are talking Jack tells him that the he doesn't really like Antarctica but Sheppard likes it. "You like it here?!

"Yes, sir," He checks his instruments. "Be there in about ten minutes, sir.

Back at the Ancient outpost, Doctor McKay is pushing Doctor Beckett back towards the Chair. "Look, we've been through this. I'm not your man."

"Keep moving," McKay tells him.

"I'm a doctor, a medical doctor. I wish Colonel Horton was here to do this?"

"So do we all, but he's not. There is nothing to be afraid of."

"You don't understand. I break things like this."

"This device has survived for millions of years intact. It will survive you. Now sit down, close your eyes and concentrate." Beckett sighs in irritation, and then sits down in the Chair. He puts his hands on the control pads on the arms of the Chair briefly. He tries to stand but McKay pushes him back down. "This time, just try to imagine an image of where we are in the solar system." Beckett sighs again and closes his eyes. He remains there for several seconds. Beckett looks at McKay for a moment, then closes his eyes. After several seconds the lights on the back of the Chair come on and the Chair reclines. As Beckett opens his eyes in panic, the drone that Peter Grodin was working on lights up. Grodin snatches his hands back in panic as McKay turns and stares. The drone shoots off its stand, flies out into the room and smashes through some equipment, which explodes and sends people flying. The drone shoots around the room some more, smashing more equipment, then heads up the elevator shaft. Beckett stares at it as it goes. The drone flies up the shaft and shoots past the elevator which is rising up the shaft. Doctor Weir is on board. She watches the drone zip past, then stares downwards and shouts at someone else on board.

"Get us back down there!" Elizabeth Weir says. The drone bursts out through the dome and heads off into the sky.

Major John Sheppard hears a voice over the radio, "All inbound craft, we have a rogue drone that could seek a target on its own. Land immediately and shut down your engines. This is not a drill. I repeat turn off your engines. The drone flies at them but Sheppard swings the helicopter out of its way. The drone circles around and comes at them from behind. Again Sheppard yanks the helicopter out of the way. Again the drone swings around and heads towards them. "Break right," O'Neill says. Sheppard banks hard to the left. The drone whizzes past them again. "I said right!"

"I'm gettin' to that, sir." He swings the helicopter to the right. Weir gets out of the elevator in the ancient outpost, looks around at the damage the drone has caused, then runs over to the Chair. Beckett is still sitting in it and looks up at her plaintively. Weir tells him to concentrate on shutting the drone down. Beckett closes his eyes, takes a deep breath and concentrates. O'Neill and Sheppard are looking around for the drone. Sheppard tells O'Neill that he can't see it that is when O'Neill tells him to pull up. He has seen the drone heading towards them from the front. Sheppard sees it and put the helicopter into a steep dive. The drone shoots over the top of them.

"What about now?" As the drone shoots underneath them, Sheppard brings the helicopter down and lands. Sheppard yanks on a handle to shut the engines down. The drone smashes over the top of a snow dune ahead of them and heads for the helicopter, which is still shutting down. They unbuckle their seat belts and open their doors. Sheppard takes a flying leap out of his door, landing face down in the snow. The drone, its internal lights no longer on, crashes into the snow and skitters across the top of it, stopping a few inches away from O'Neill who is sitting on the snow just outside the helicopter door. O'Neill stares at it for a moment, and then cautiously sits up.

Beckett gasps and opens his eyes, staring in amazement. "I think I did it!" Weir sighs in relief.

Sheppard's uniform is covered in snow, walks back to the helicopter and gets back in as O'Neill gets in the other side. They sit there for a moment, a little breathless and stunned. "That was different."

"For me, not so much," O'Neill replies. Lieutenant Aiden Ford runs over to report to Doctor Weir.

"Major Sheppard is reporting the drone appears to have been incapacitated." Weir sighs in relief. Beckett, still sitting in the Chair, does likewise. "General O'Neill's helicopter is unharmed and on its way again. Seven minutes out." Daniel Jackson walks over to the elevator as O'Neill and Sheppard get off it.

"Jack!" Daniel says.

"Daniel! Warm welcome," O'Neill says to him.

"Wasn't me. How did you manage to, uh ...?""

"Keep my ass from gettin' blown out of the sky?" He turns and gestures to Sheppard. "The exceptional flying of Major John Sheppard. He likes it here."

"Exceptional." He looks at Sheppard in surprise. "You like it here?" Sheppard shrugs. Jack turns to Daniel as the two of them start to walk away.

"What say we skip to the part where you start talking real fast?"

"Ah. Weir's in here." O'Neill tells Sheppard not to touch anything. Doctor Daniel Jackson, General Jack O'Neill, Doctor Rodney McKay, Doctor Elizabeth Weir are discussing what to do now General O'Neill agree at first until he finds out that they need the ZPM.

Sheppard is still wandering around. He walks over to the Chair Room and overhears Beckett talking to a couple of people. "The second I shut my eyes, I could see. I felt power I've never had before. I had it dancing all across the sky. It was magical, it really was." He laughs. "They're lucky. I don't know where it came from. I just tried to concentrate and the drone shut itself down." He laughs again.

"So you were the one." Beckett turns to him nervously. "You were the one who fired that thing at me."

"Look we're doing research; working with technology that's light years beyond us and we make mistakes. I'm incredibly, incredibly sorry."

"Well, next time just be a little more careful, OK?"

"That's what I said."

"What the hell was that thing anyway?"

"You mean the drone? The weapon the Ancients built to defend this outpost."

"Who are u talking about?"

"You do have security clearance to be here?"

"Yeah, General O'Neill just gave it to me."

"Then you don't even know about the Stargate."

"What is a Stargate?"

"They think the gene was used as a sort of genetic key, if you will, so that only their kind could operate certain dangerous and powerful technologies." He turns away from the Chair. Behind him, Sheppard pokes at the arm control panels tentatively.

"So some people have the same genes as these Ancients." He walks around the Chair.

"The specific gene is very rare, but on the whole they look very much like we do. In fact they were first. We're the second evolution of this form, the Ancients having explored this galaxy for millions of years before Major, please don't." Sheppard has started to sit down in the Chair.

"Come on, what are the odds of me having the same genes as these guys?" As he sits down, the Chair immediately lights up and reclines. Both he and Beckett stare in amazement.

"Quite slim, actually," Carson says. "Doctor Weir!" He looks at Sheppard. "Don't move." He hurries off. Sheppard lies in the Chair, looking upwards nervously. Beckett and the others run back to the Chair. Weir stops and looks at Sheppard.

"Who is this?" Weir asked. O'Neill walks up onto the dais and looks down at Sheppard.

"I said don't touch anything."

"Major, think about where we are in the solar system," Rodney McKay says to him. A holographic three dimensional map of a star system appears above Sheppard's head. Everyone gazes up at it. Weir smiles in delight. Sheppard looks up at the map, frowning.

O'Neill is walking through the outpost with Weir. "We could be on our way to discovering an entirely new Ancient civilization. At the best case scenario, we meet actual Ancients who are willing to help us, but if we don't." She trails off as she realizes that O'Neill isn't paying attention to her. "General, we need him."

"Sorry, Doc. I need Daniel here."

"I'm talking about Major Sheppard." She tells him.

"Oh. Don't you have a dozen or so people already who can use the Ancient technology?

"Yeah, with concentration and training they can make it work, but John Sheppard, he does it naturally just like Colonel Horton."

"You know, I checked into his record."

"I know about the whole supposed black mark in Afghanistan. He was trying to save the lives of three servicemen."

"Disobeying a direct order in the process."

"I have read your own file, General. Please." Weir says smiling.

"Right," he says. He glances at her uncomfortably, blowing out a breath. "OK. It's your expedition." He boards the elevator.  
You want him, you ask him." Weir says she did and that he didn't give her answer. General O'Neill and Major Sheppard are discussing it during the pre-fight.

Everyone who is going on the Atlantis Expedition is at Stargate Command. Lieutenant Ford is struggling to communicate with a couple of people. Major John Sheppard is making his way through the tight hallways of the SGC. Doctor Beckett is arguing with Sergeant Bates.

"I just need a couple of minutes to finish my work, and you're not helping by standing there."

"You got five minutes to get it going or I'm leaving it." Colonel Marshall Sumner walks down the ramp that leads to the Stargate and goes over to the pair of them.

"Everything in here has been double checked and triple checked and cleared for takeoff. Leave it alone."

"Look, Colonel, I don't answer to you." Carson tells Colonel Sumner.

"He said the same to me, sir." Bates tells the colonel.

"That's what your sidearm's for." He walks back onto the ramp as Beckett and Bates glare at each other. Doctor Weir is watching all the activity down in the Gateroom as Daniel walks in explaining something to a female scientist. Colonel Horton and Major Jason Halsey geared up and wearing a large backpack and carrying P-90s, walk into the Gateroom. He sees Colonel Sumner inside talking. Colonel Sumner is Colonel Horton's second in command. Just then, Weir walks into the Gateroom.

"Could I have everyone's attention please?" Wearing a small backpack, she walks up the ramp and turns to face everyone as they gather round. In the Control Room, Daniel stands up and walks over to stand next to O'Neill. They both look down into the Gateroom as Weir addresses the expedition members.

"Alright, here we go. We are about to try to make a connection. We have been unable to predict exactly how much power this is gonna take and we may only get the one chance at this, so if we are able to achieve a stable wormhole, we're not gonna risk shutting the Gate down. We'll send in the M.A.L.P robot probe, check for viability and go. Everything in one shot. Now, every one of you volunteered for this mission and you represent over a dozen countries. You are the world's best and brightest; and in light of the adventure we are about to embark on, you are also the bravest. I hope we all return one day having discovered a whole new realm for humanity to explore, but as all of you know, we may never be able to return home. I'd like to offer you all one last chance to withdraw your participation." Some of the expedition members look around at each other, but nobody moves. Weir smiles, then looks up to the Control Room. "Begin the dialing sequence."  
She walks off the ramp as alarms sound and the Gate begins to spin. As Sheppard checks his equipment, Sumner walks over to stand beside him.

"Let me make myself clear, Major, You are not here by my choice."Sheppard smiles ironically, rolls his eyes and speaks without looking at him.

"I'm sure you'll warm up to me once you get to know me, sir."

"As long as you remember who's giving the orders." He walks away.

"That would be Doctor Weir and Colonel Horton." Sumner turns to stare at him as a couple of marines clip his backpack on. Sheppard smiles at him. Sheppard holds his smile for a moment but Sumner just glares at him. Finally Sheppard looks away and rolls his eyes again. Colonel Horton has a smile on his face. They send the MALP through first and determine it was safe to continue. General O'Neill wished her good luck and told her mission is a go. In the gateroom Colonel Sumner is getting everyone ready to go.

"Let's go, people. We don't know how much time we've got." He walks up the ramp, followed by some marines. "Security teams one and two, you're up first. All other personnel will follow on our signal. Once on the other side, keep moving, clear the debarkation area." Colonel Horton looks at Colonel Sumner he knows the marines and army don't get along very well and Sumner hates him for some reason maybe because the President place his son in command of the military on the expedition with the approval of Doctor Elizabeth Weir of course. Colonel Horton decided him and his men along with two marines part of his team would be the last ones through the gate along with heavy weaponry to defend whatever installation they find for whatever enemies they encounter. He walks to the top of the ramp with a couple of other marines, raises his P-90 and aims it forward, then walks into the wormhole. Sergeant Bates and another marine follow him, their weapons also raised. As another marine enters the wormhole, Weir stops at the top of the ramp and looks back at the Control Room, O'Neill nods to her. She nods back, then turns and steps into the wormhole. Ford and Sheppard are next once Sumner reports all clear from the other side. At the other end of the wormhole, Sheppard steps out into a darkened room. The marines who already went through are cautiously checking out the area. Directly ahead of the Gate is a flight of steps leading up to another floor. Somewhere on the upper level, lights started to come on. Colonel Sumner tells the two teams of marines that came through with him to secure the immediate area. Scientist, marines, and air force began coming through the gate carrying their gear and large cases of different things. Weir is standing in the middle of the Gateroom, gazing around the room. Sheppard and McKay head towards the steps. As Sheppard puts his foot on the first step, the stairs light up.

"Who's doing that?" Weir asks.

"Security teams: any alien contact?" Sumner says into his radio. Negative reports come back over the radio. They began uncovering the controls in the control room. Colonel Horton and his men enter with the heavy weapons and the last two through the gate are marines. That is when Colonel Horton tells Elizabeth that's everyone. Weir turns towards the Gate and lifts her radio to her mouth.

"General O'Neill. Atlantis base offers greetings from the Pegasus Galaxy. You may cut power to the Gate." A champagne bottle rolls out of the Gate and across the floor. The Gate shuts down. Weir picks up the bottle and looks at the label attached around its neck. It reads: "Bon Voyage! General Jack O'Neill". Weir smiles around especially up on the balcony where Rodney, John and Heath are and they are looking back at her. The military personal began searching and lights began coming online. In another area, two scientists have entered a room and found a small lozenge-shaped ship inside. They walk to the front and peer in through the windshield. They call the objects spaceships. They radio back to Doctor Weir and tell her that she has to see this. She tells them she has lots to see and to be careful. She walks back into the room with the consoles, where McKay is taking the sheeting off another one. Nearby, Sheppard is wandering around the room. As he approaches a screen on the wall, it activates and blue light starts to scroll across it. Sheppard turns and raises his hands to Weir. John looks at Elizabeth.

"Relax, Major. It's like the entire complex is sensing our presence and coming to life," She says.

"This has got to be the Control Room," Rodney says. He looks down at the console. "This is obviously their version of a D.H.D." McKay looks around and starts guessing what each console is until Elizabeth tells him to find out. Colonel Sumner contacts them and asks for Elizabeth and Heath to come and meet him. John comes with them. He tells them they have only secured a portion of the city and that's it huge." He leads them towards what he wants them to see. Weir stares in amazement. They see that they're under water, Rodney shows up telling they're under water and that a forcefield is holding back the water and Doctor Beckett wants to show them something. McKay leads the others into a room. A glowing hologram of a woman in a white robe is talking.  
This is what the hologram said; "in the hope of spreading new life in a galaxy where there appeared to be none. Soon the new life grew, prospered exchange knowledge and friendship." A three dimensional holographic map of the galaxy appear overhead. "In time, a thousand worlds bore the fruit of life in this form. Then one day our people stepped foot upon a dark world where a terrible enemy slept. Never before had we encountered beings with powers that rivaled our own. In our over-confidence, we were unprepared and outnumbered. The enemy fed upon defenseless human worlds like a great scourge until finally only Atlantis remained. This city's great shield was powerful enough to withstand their terrible weapons but here we were besieged for many years. In an effort to save the last of our kind, we submerged our great city into the ocean. The Atlantis Stargate was the one and only link back to Earth from this galaxy, and those who remained used it to return to that world that was once home. There, the last survivors of Atlantis lived out the remainder of their lives. This city was left to slumber, in the hope that our kind would one day return. Peter Grodin hurries in and walks over to McKay, whispering something in his ear. Carson steps back onto the podium but Rodney tells him to stop and that they're losing a lot of power and if they don't stop they're dead.

They return to the control room. Rodney gets busy working on a laptop; Heath sits down on a laptop too. Heath is very smart like Carter and McKay but he's a military man like Sheppard and O'Neil but he can still be a geek at times. "What we've been able to ascertain, the city is powered by three Zero Point Modules. Two are entirely depleted and the third is reaching maximum entropy. When it does, it'll die too and nothing can reverse that." Rodney tells them. Weir looked at Heath. Heath nods back as if confirming Rodney's statement.

"What's the bottom line?" Colonel Sumner asks.

"The ZPM is powering the forcefield which is holding back the water and once it fails we drown," Heath replies. "Colonel, order all security teams to fall back to the gateroom." He nods and gives the order. Sumner suggest using the gate but McKay tells him there isn't enough power to gate back to Earth but Sheppard suggest they use the gate to go somewhere in the Pegasus Galaxy." Rodney leads Weir and Sheppard over to the console that acts as a D.H.D., where Grodin is already working. "Fortunately some Ancient technology still uses good old-fashioned push buttons, so we've been able to access the Stargate control system and a library of known Gate addresses in the database."

"That's not all. Look at this," Grodin says. He pushes a button and a shimmering force shield appears across the Stargate.

"Just like the iris on the Earth Gate," Sumner says.

"Using power, using power, using power," he says quietly and pointing. Grodin finally realizes what he means and shuts the shield off.

"At least we don't have to deal with any uninvited guests," Weir says. She turns to Heath. "Colonel, assemble a team. We need safe harbor, or better still another power source." Heath turns to Sumner and gives him the order.

"Lieutenant Ford, gather security teams one and two. Everyone gear up," Sumner says into his radio.

"Major, I want you to go along," she says to him.

"Yes Ma'am," he replies.

"Glad to have you with us John," Heath says to him. They head down into the control room.

"Alright, Pick an address, start dialing." McKay reaches down and pushes one of the glass panels on the D.H.D. Lights run around the symbols on the Stargate, then the first chevron lights up.

"Chevron one encoded," Rodney says doing like Walter does at the SGC. Weir blinks, and then looks at McKay. He looks at her, realizing that this routine isn't necessary. He pushes the next five panels in more rapid succession. Lights run around the Gate and the corresponding chevrons light up.

"Ready M.A.L.P Four for offworld recon," Grodin says in his radio. McKay pushes the central panel on the D.H.D. Lights run around the Gate, the top chevron lights up and the Gate kawhooshes. Grodin grabs a case from the floor and runs down the steps into the Gateroom. The search teams enter the room. Weir and McKay walk to the edge of the Control Room balcony and look down into the Gateroom. Grodin checks a small handheld computer.

"M.A.L.P. reads full viability and no immediate signs of activity around the Stargate, but its pitch black." He tells them. The team starts to put on night goggles, leaving them up on their foreheads for the time being. "For now, we're going to use the tried and true system for identification for inbound Gate travelers." Colonel Summer is taking a team through the gate and Major Sheppard is going with them.

"Colonel Sumner, please come here," Horton calls.

"Sir," Colonel Sumner replies.

"Show some respect for the major, or you'll have me to answer too. I don't care what is record is or how he doesn't follow the proper chain of command. I would have done the same thing if I was in his place."

"Yes sir," Sumner replies. Heath can tell he didn't like what he told him, but he didn't care he need his military officers to work together if they're to be successful on the expedition. They placed their night vision goggles on and they go through the gate. Colonel Horton remains behind on Atlantis to help Rodney try to stop the forcefield from collapsing. Colonel Sumner and the others meet the Indigenous people. They follow Holien and Jinto to their camp. Colonel Sumner and Major Sheppard talked with Teyla. The next day The Wraith showed up and started to cull the planet. Marines shot down one of the enemy flying ships. They took Colonel Summer and several marines hostage along with Teyla and other Athosians.

Back on Atlantis, Weir walks into the control room and looks at Heath and Rodney both shake their heads. "We need to go now," Rodney says.

"We have yet to hear from Colonel Sumner. We've got no idea what's out there." Weir says.

"Elizabeth, Rodney's right, we have to leave I'm sure the Ancients got another place we can use as a base until we find a new power source," Heath says. "My team is ready to go." Frustrated, Weir walks away from him, and then activates her radio. She tells Rodney to dial the gate, but he doesn't get the second chevron when they get an incoming wormhole. The force shield comes on and the Gate activates.

"I'm reading Lieutenant Ford's identification code," Grodin says. McKay lowers the shield. Sheppard comes through the Gate, followed by the rest of the marines and the Athosians. Weir runs down the steps to him follow by Heath.

"Major Sheppard, who are all these people?" Weir asks.

"They're refugees from the planet we were attack they took some of our people including Colonel Sumner. The city shakes again.

"We need to evacuate," Weir says.

"Going back there is a bad idea," he says. The city shakes again. They ascended to the surface of the water. "You wanted another day we just got more than that," Dr. Weir tells them.

"We're on the surface," Lieutenant Ford tells them.

"Yes, lieutenant I can see that," Colonel Horton replies. They started to unpack. "Now that we're on the surface our generators will provide power to the city."

"That's good, what about the shield?" Sheppard asks.

"Not even close," Heath replies. Colonel Horton and Dr. Weir argued over rescuing their people, and then Major Sheppard joined him.

"What do we know about the Wraith?" She says. "One of the things we do know they're the race that defeated the Ancients. They continued to argue. They send a MALP through the Stargate and found out it's in space.

"Sorry," Dr. Weir tells the colonel and the Major.

"Come with me major, colonel," McKay tells them. They get in one of the ships. "Can you fly it?"

"Let's find out," the major replies.

"Colonel goes try another one," McKay suggested. They go try both of the ships. Meanwhile Dr. Weir goes to see Dr. Beckett. "Dr. Beckett you wanted to see me," Dr. Weir says to him. He tells Dr. Weir about the arm Major Sheppard brought back.

"They'll be hard to kill," he tells her.

"That's scary," Dr. Weir replies.

"Aye," Dr. Beckett replies. Dr. Elizabeth Weir allowed them to go rescued their people when she sees the edge the ships give them.

They are in the ships. "Gate ship one ready for takeoff," Lieutenant Ford says to Major Sheppard. The colonel sits down behind the major, three marines and two army rangers are in the back.

"Gate ship one, a little buddle jumper like this," Major Sheppard replies surprised at the comment.

"McKay thought it was cool," Ford replies.

"Well, you don't get to name anything ever," Sheppard replies. The Lieutenant just looked at the colonel. He just nods his head. "Flight this is Puddle Jumper, we're ready for lift off," Sheppard replies over the com.

"This is flight I thought we were going with Gate Ship," McKay replies.

"Negative flight," Sheppard replies.

"Standby," McKay tells them. Dr. Weir looks at him. "It's a ship it goes thought the gate. Fine, Puddle Jumper 1 you're ready for lift off."

"Dial it up lieutenant," Major Sheppard tells Lt. Ford. Lieutenant Ford dials up the gate with the Jumper's gate dialup. They go through the gate.

Meanwhile on board the Wraith ship. A Wraith commander came to bring Colonel Summer to the Queen. "Why have you taken my people?" Colonel Summer asked the queen.

"You've trespassed upon our feeding ground," the queen replies. The queen began interrogating him. "What planet are you from?" The queen demanded from him. He did not answer, but she made him with some type of mind control. "How many people are there on your world? Hundreds, thousands, and millions, more?" He still did not answer, but she could tell that there are more. "Our feeding ground has not been rich in over ten thousand years."

Sheppard, Ford, Horton, army rangers, and the marines arrived through the gate. "A lot of fighter pilots would give to fly this, it's like it reads your mind," Sheppard tells him. A screen pops up.

"Did you do that?" Ford asked him.

"I just wonder where we go now," Sheppard replies.

"I guessed that answers that," Colonel Horton replies.

"How do we find them once we land?" Lieutenant Ford asked.

"I been thinking about that too," he answers. A panel opens on Sheppard left. "Now I'm thinking of a nice turkey sandwich."

"Worth a try," Lieutenant Ford replies. They land. Colonel Horton, Sheppard, and Lieutenant Ford headed for the Wraith ship. They get aboard the Wraith ship. A Wraith pasted by. "That's the first one we saw."

"Spread out," Sheppard tells them. They spread out. "Okay that's him and that's us."

"Looks like we have a life signs detector," Ford tells them.

"We can name it later," Major Sheppard replies. They continue to move through the ships. They find the others.

"Where's Colonel Summer?" Major Sheppard asked them.

"The Wraith took him," Sergeant Bakes replies. They give them C4 so once the C4 is detonated they can escape. Colonel Horton and Major Sheppard went to go look for Colonel Summer. The Wraith started to feed on the colonel, therefore, Sheppard was able to locate him by his screams. He shoots the queen. She feeds off Colonel Summer to heal herself. John kills a Wraith guard. Major Sheppard kills Colonel Summer but is stun from behind by another Wraith commander. They bring him before the queen. The queen starts to interrogate him but his reply is I don't remember. Colonel Horton tries to rescue him, but is also captured but not before two Wraith Warriors is killed. The queen/caretaker goes over to Colonel Horton, she tried to use her telepathic powers on him but it somehow has no effect on him. She decides to deal with him later. The queen was fixing to feed on Major Sheppard, but Lieutenant Ford kills several Wraiths. He rolls off the table and tells them to light it up. The colonel picks up his P90 and kills another Wraith entering the room. Major John Sheppard kills the Wraith queen and then they escaped. They returned to the ship. Colonel Horton gets into the pilot seat.

"Sir, do you know how to fly," Major Sheppard asked him. The colonel only nods his head. They take their seats. The colonel did some excellent flying and destroyed several Wraith fighters. They escaped through the Stargate. They arrived back on Atlantis and they raised the shield. The Wraith fighters ran into the shield and were destroyed. They had a celebration about their arrival on Atlantis and the new friends they made.


	2. Chapter 2: BR666

Authors Note: This is a new episode to Season 1 of Stargate Atlantis.

Chapter Two

BR666

One week after arriving in Pegasus this is Heath's second off-world mission in a new galaxy but for most of his off-world team his is the first in the new galaxy. He has served at the SGC for several years before Doctor Elizabeth Weir recruited him for the Atlantis Expedition. Colonel Horton, his team and a marine team along with Dr. Jay Cake arrived on BR666 through the Stargate. The colonel's NCO is Master Sergeant Garrett Howzer. "Sergeant, secure the area." Colonel Horton ordered.

"Sir Yes sir," the Sergeant replies. "Marines, you heard the colonel secure the gate!" They spread out securing the area.

"Sergeant instructs your men to set up base camp, I only need three men to accompany me," the colonel tells Sergeant Howzer.

"Corporal Chelsea Hart, take PFC Oliver, PFC Sarah Scott, Private James Neman, Private Lee Gainey stay here and setup a base camp," the sergeant tells them. Therefore, Master Sergeant Garrett Howzer, Staff Sergeant Geoffrey Rhodes, Lieutenant John, Corporal Craig Farte, and Dr. Cake are following the colonel. They climbed a hill, once at the top Colonel Horton took out his binoculars.

"There's a structure in the middle of the forest," Colonel Horton tells them.

"Are we going to go there?" Dr. Cake asked.

"Not tonight," the colonel replies. They headed back to the base camp. "Lieutenant, head back to the gate and tell the good doctor what we found tell her to send the rest of my team through." The lieutenant headed back to the gate. He tells Dr. Weir and she sends the rest of Colonel Horton team through the gate. Once back at base camp, he gives his report to Colonel Horton.

"Sir, Dr. Weir has suspended all gate operation to and from Atlantis because Major Sheppard team keeps getting attack by Wraith off world," the lieutenant tells him.

The following day Colonel Horton and his team along with the marines headed to the structure in the middle of the forest. Somehow they alerted the Wraith to their presence. They reached the structure by mid afternoon. Colonel Horton recognized the structure to be made by the Ancients. They started to explore the structure. Once Colonel Horton stepped into the structure the lights came on. "We're going to split up and check this place out. Lieutenant, leave two men to guard this entrance." The Colonel tells Lieutenant John.

"PFC Jimmy Hart and Private Newman remain here and guard this exit." The lieutenant tells them.

"Yes sir," they replied. The rest headed inside. Dr. Cake along with Master Sergeant Garrett Howzer, PFC Sarah Scott, and Corporal Chelsea Hart went one way. Colonel Horton, Staff Sergeant Geoffrey Rhodes, Corporal Griffin, and Private Lee Gainey went another way. The others went another way. Dr. Cake and his team found more puddle jumpers. "I wonder if they have any ZPMs here." The sergeant asked Dr. Cake.

"Let's go find out," Dr. Cake replies. Therefore, they went to see if there were any ZPMs in this structure.

"Colonel, you have to come see this," Major Jason says over the radio.

`"What did you find Jason," the colonel replies.

"Sir, we found the control room," Jason replies.

"We'll be right there." Therefore, they head to the control room. "Dr. Cake please report to the control room." They arrived at the control room.

"What is it major," the colonel asked him.

"Sir, the outpost long range sensors have detected several Wraith ships heading this way." Major Jason answers. Dr. Cake and his team arrived.

"Does this outpost have a ZPM?" Colonel Horton asked them.

"Yes sir," Master Sergeant Garrett answered. "Four ZPMs actually."

"Good, we're going to need them," the colonel replies.

"Why sir?" Dr. Cake asked.

"We have Wraith on the way," Major Jason answers.

"Major we must prepare the defenses of this structure. Doctor I want a blueprint of this base ASAP. Lieutenant, I want you to see if this structure has a weapons platform similar to the one found in Antarctica and see if it has any Drones left. Master Sergeant Garrett you'll accompany me back to the Gate we must inform Dr. Weir of our situation besides we are almost due to check in any way we must not let this outpost fall into Wraith hands," the colonel tells them. Therefore, the colonel and Master Sergeant Garrett headed to the gate. Major Jason got the others preparing defenses. It took hours to reach the gate and it was almost getting dark. The colonel started to dial the gate while the sergeant covered him. After he dialed the first two gate icons, more light lit up. "Incoming wormhole!" They took cover in the woods. Wraith stated to come through the gate. Once the last Wraith was threw the gate shut down. The colonel estimated four dozen Wraith. "Let's get back to the structure." The colonel suggested.

"Let's go sir," the sergeant replies. They headed back to the structure. The reach for the night vision goggles in their packs. The colonel brought out a life signs detector. "Are we clear sir?" The colonel looks at the detector.

"Negative, we got six headed our way, they're almost here," the colonel replies.

"What are we going to do sir?"

"We're going to kill them," the colonel answers.

"Now you're talking." They took cover off the trail. A few minutes went by the six Wraith started coming down the path. The colonel and the sergeant used hand signals to communicate. The colonel took careful aimed at the Wraith leading them. He shot the Wraith in the head, and then they opened up on the others. They threw grenades it took a lot of rounds to dispatch them, but they manage to kill them all. Then they continued on to the structure. Lieutenant John was out on patrol with several marines. They found the colonel and the master sergeant. Lieutenant John escorted them back to the structure. They returned to the control room.

"Report major," the colonel says to him. "Sir, seventeen Wraith ships just emerge from hyperspace. This base does have an ancient platform like in Antarctica but it only has sixteen dozen Drones," the major responds. "What did you find out sir?"

"They have troops coming through the gate," the colonel tells them. "Dr. Cake have you got a blueprint of this place yet?" The Doctor brought up a blueprint on the screen. The colonel found a perfect place to hold the Wraith up for maybe a couple hours. They go where they enter the structure and looked up. There's a balcony above them and the doors can be closed that go further into the structure. Therefore, they start to set up barricades from anything they can find in and out of the structure. They planted claymores outside of the structure where the enemy will have to come up to get into the structure. They planted C4 inside of the structure where they are going to ambush the Wraith. Colonel Horton went to the control room to talk to Dr. Cake. "Dr. Cake I need you to find a way to destroy this structure and the Ancient database in case we cannot stop the Wraith." Colonel Horton tells him.

"The Ancient Database has a lot of stuff in it we can't destroy it," Dr. Cake tells him.

"Then you better find a way to store it somewhere else otherwise we will have to destroy it." The doctor nods. Then the colonel headed to the Ancient weapons chair. Private Newman remained in the control room.

"Colonel they're launching fighters," Private Newman tells him.

"Bring up the shield," the colonel tells him. Private Newman pressed the button to open the shield. The colonel fired the Drones at the Darts, but he sent some to destroy as many ships as he could in space. Darts ran into the shield and were destroyed. More Darts and transport ships are coming down from the ships in orbit. The colonel fired the last dozen Drones. Three Drones destroyed three transport ships. He only destroyed two Wraith Hive ships in space. The last reaming Drones he instructed to destroy the Darts. He headed to the ambush site. The transport unloaded hundreds of Wraith soldiers in each transport that landed. Master Sergeant Garrett and his men are on one side of the ambush site on the balcony. Major Jason and his men are on the other side. Colonel Horton arrived and took his place along with Jason. "No fire until I fire," the colonel says over the radio.

Meanwhile on Atlantis Major Sheppard and his team just arrived with a Wraith prisoner. Another team of Marines escorted the prisoner to the holding cells. Doctor Elizabeth Weir came up to Major Sheppard. "Is there something wrong?" Sheppard asked her.

"John, we haven't heard from Colonel Horton team for hours they missed their schedule check in," she tells him.

"You want me to take a team to find out what's keeping them?" Sheppard asked.

"Yes," she replies. Major Sheppard, Lieutenant Ford, Rodney McKay, and Teyla headed to the jumper bay with another team of Army Rangers lead by Lieutenant Michael. They dialed the gate and went through. They emerged through the gate. They see Darts in the air; therefore, they cloaked the ship.

"Colonel Horton please come in, this is Major Sheppard." He says over the com. He repeated several times.

Before they came through the gate the Wraith attacked the structure first by orbital bombardment and Kamkazzie runs with their fighters. It did not take long for the shields to fall. Then the ground forces attacked the structure. They believe the Ancients were here. They hit claymores outside, but it did not stop them. They ran into the structure and realized they were trapped. Colonel Horton shot the leader of the first wave in the head. The reason you can tell they are leader is because you can see their faces. Then the rest opened up. The Wraith returned fire, but hit nothing. One marine fired is grenade launcher killing three Wraiths. Then more Wraith entered the structure. They continued to fire."Sir, we're going to run out of ammunition if we keep this up," Major Jason tells the colonel. They continued to fire. Colonel Horton heard Major Sheppard's message over the radio.

"Major Sheppard we're in the structure Wraith everywhere, you can enter through the Jumper bay."

"They have a Jumper bay?" McKay asked. No one answer. Therefore, Sheppard flew the Jumper to the Jumper bay. Sergeant Garrett kills several more Wraith before he ran out of ammunition to his P90.

"Hit the C4," Lieutenant John ordered. They hit the C4 remotes killing even more Wraith, but they still kept coming inside.

"Fall back to the control room," the colonel ordered. They returned to the control room where Major Sheppard and his team were waiting for them. "Let's get the hell out of here!" They sat a huge C4 bomb in critical areas of the structure. Dr. Cake, have you taken care of the Ancient Database?"

"Yes Colonel," he replies.

"What about the ZPMs?"

"Fully depleted sir," Private Newman replies.

"Dam we could've use them on Atlantis." Then they headed to the Jumper bay. Only Colonel Horton, Major Jason, Major Sheppard, and Lieutenant John can pilot the Jumpers really well. They all get into several jumpers. They open the Jumper bay doors and had to destroy several Darts before they could leave. They cloaked once they were in the air. Major Sheppard dialed the gate and they follow him threw. Once they were safety on Atlantis the shield was raised and they could see were an explosion took place behind them from the color of the shield.


	3. Chapter 3

Chapter 3

PX1W32

Colonel Horton arrives at the gate room just in time to see Colonel Sheppard's team leave on a mission to M7G-677 in a Puddle Jumper. "Aye colonel just the man I wanted to see." Doctor Zelenka says.

"What can I do for you?"

"We've been going over some of the data you brought back from BR666 and we may have found something but Doctor Weir wants to discuss a possibly of seeing if there are ZPMs there." Colonel Horton heads to the conference room. Doctor Elizabeth Weir and two others are present including Doctor Carson Beckett. He sits down. Doctor Zelenka sits down as well who just entered.

"Colonel I like you to take a team to PX1-W32 and see if they have any ZPMs or anything we can possibly use to help us fight the Wraith."

"Yes ma'am," Colonel Horton responds.

"Doctor Zelenka will be accompanied you," she tells him. colonel Horton goes and get his team ready for their off-world mission. doctor Zelenka accompanies him. they enter the armory where his team is already gearing up. Sergeant Major Howzer is present too. He hands Heath his tactical vest and P90.

"Hey doc have you ever fire a gun before?" PVT Shaw asks. Zelenka shakes his head. Sergeant Major Howzer comes up to him and shows him the working of a Beretta 9mm. Radek Zelenka takes a vest put he's also taking a laptop with him. They head back to the gate-room. Peter Grodin dials the planet and the team goes through.

They emerge in a large room as soon as the gate shutdown it complete black they activate their flashlights. "Stay alert," Colonel Horton tells them. their where whisper replies. they moved sweeping the area with their flashlight but see no signs of anything. Two marines wonder off.

"Sir, you might want to see me we've found some sort of control room," a soldier radios.

"We'll be right there don't touch anything," Heaths says. They arrive. Heath shines his flashlight around and notice he design to be Lantian in nature. Heath goes over to the console and as if sensing his ATA gene, the console and the everything turns on.

"We must be in an Ancient facility," Private Newman says.

"Nah dah," PFC Sarah Scott says.

"That's enough," Sergeant Major Howzer says. Doctor Zelenka goes over to the console. I'll bring up a map of the base. He pulls up the map.

"Colonel, I found something interesting according to this the facility has two ZPMs."

"Where are, they located?" Zelenka shows him on the map. Colonel Horton gets three me to accompany him to where the ZPMs are located. As they're heading their they come across a big window and Colonel Horton happens to look out and realized they're in some sort of Ancient space station on an asteroid or moon. He radios Zelenka. "Hey Radek did you know we're in space?"

"Colonel, we're on an asteroid in space," he answers.

"Sir, we have an asteroid base," Corporal Chelsea Hart replies.

"we'll name it later," Heaths says. they head towards a door that leads to the power/ZPM room. They enter the power room. Heath goes over to the console and taps on it and 2 ZPMs rise. He activates his radio, Radek get down here let's see how much power they have left?" Radek heads down to the power room with Corporal Griffin and PFC Gainy. They arrive. Zelenka goes to work he inserts a data cable into a port on the Lantian console, "this should take a few minutes." Radek tells them.

"Bingo," he says. "Well colonel I got some good news and bad news." He looks at the computer screen. "There is only one ZPM left and its only at 10%."

"Have you discovered what this facility is use for?"

"In a way, it's a base for the Lantian Fleet, but there are no ships here. They have two control chairs and the base is fully stock with Drones plus some sort of other defensive and offensive armaments."

"Let's go inform Doctor Weir what we found," Heath tells him. They return to the Stargate and dialed Atlantis. Heath tells Doctor Weir what they found and she asks for his suggestion. He tells her the facility could be a good fallback point or Alpha Site if they should abandon Atlantis and they can always pull the ZPM later. She agreed with his assessment. He tells her they would like to stay a while and explore the facility. She agreed. The gate shuts down.

Trouble began when the facilities long range sensors picked up Wraith ships in the area however no one was in the control room when the sensors picked up the Wraith ships. However, Heath does discover some Wraith bodies and something blinking. He realized it's a distress signal. He understood the Wraith can be on their way. "Pack up we're leaving." He informed them of the situation and as soon as they arrived at control room they see the Wraith ships on the sensors.

"What about the ZPM," Sergeant Major Garret Howzer asks.

"Sir Darts inbound along with two other ships I don't know what they are," PFC Gainy says. we need to put the facility back into dormant and lock the controls with only someone with the ATA gene can get it back online.

"I think there might be a way," Zelenka says. "Come over here colonel." He goes over to where Radek is standing.

"Darts and whatever are landing and deploying troops," PFC Gainey tells them.

"Sergeant Major buy us sometime," Colonel Horton tells him.

"Yes sir," he replies. heath touches the control. "Dormant stage, temporary lockdown of all systems except Stargate Lantian DNA required to begin. Heath place his hand on the console. Same voice appeared. "DNA match beginning Time of completion 45 minutes. Please keep hand on console until completion." Wraith Warriors and commanders are moving through the base. One of the Wraith looks around like he been here before. He shouts something to the warriors and their pace quicken.

"I wish we could have got to the power room and pulled the ZPM," Zelenka says.

"Then we would be trap here because without the ZPM we couldn't power the gate and the Wraith would just have some food." Heath says. "We'll return one day." Sergeant Major Garret Howzer has the men in positions hopefully they can buy the colonel enough time. A few minutes' pass and the first Wraith appeared. One of the marines is laying down with sniper rifle. He fires blowing a huge hole into a Wraith warriors head but that's not all he kills the warrior behind him. he pulls back the bolt and chambers another round and fires again killing another one. That's when all hell broke loose. Red bolts came flying towards them striking two men. A medic goes over to them and checks their pulse and shakes his head. Unknown to them at this moment these Wraith are part of the Wraith Empire and are the personal bodyguards of King Death a member of the Wraith Council and loyal friend/advisor to the emperor. After a few minutes, they're force to retreat. Four men/women are killed in the exchange. Zelenka attempts too shut the control room/Stargate doors and he gets them shut. "Dormant stage complete." Heath removes his hand from the console.

"Dial Atlantis and hurry," Colonel Horton ordered.

"Be advise only a Lantian can reactivate the facility." Private Newman dials the gate they can hear the Wraith trying to get through. The gate activates. Heath sends his IDC through. Heath orders them through. Zelenka and several marines go through first. A hole appeared in the door, but PVT. Chelsea Hart throws a grenade through the hole and is rewarded with scream but as soon as she moves away the door opens and a stun blast hits her. Sergeant Major Garrett Howzer and several others fire on the opening door cutting down several Wraith Warriors. Colonel Horton goes and picks her up throwing a flashbang into the mist of Wraith which hopefully blind them for a few seconds. He orders the sergeant major and the others to go through the gate now. They do as the colonel orders. As soon as he gets to the gate a Wraith Commander enters and looks into the colonel's eyes. He goes through the gate before a stun blast could hit him. as soon as they're through the gate the gate shield is raise. A medical team is summoned to the gate-room. Doctor Weir summons him to her office. He explains it to her. She nods after he tells her.

"Sorry about your men colonel," she tells him.

"thank you, ma'am," he replies. He leaves. John Sheppard follows after him. Rodney wasn't happy about it though he looked at Elizabeth.

"You know Elizbeth that's the second time he found a Lantian Facility and had to leave it behind because of the Wraith."

Back on the facility King Death arrived. The Wraith Commander comes up to him and goes to one knee. "Milord, we received the distress signal when we arrived in the system it must have been broadcasting for 10,000 years." King Death knew he was lying since he lead an attack on the facility 10,000 years ago, he planted something to send warning if Lantians ever return.

"Where their Lantians here?"

"No milord, but humans and their leader."

"What about their leader?"

"His eyes milord its him." The Wraith Commander looks at King Death. King Death cuts off the commander's head. King Death returns to his ship.


End file.
